Here is a good blog post about implementing command-line parameters for applications installed through ClickOnce:
This should allow us to implement a UI-less command-line interface for Skyline for use in QC and instrument control settings.
One key example of a command line would look like:
"%userprofile%\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\MacCoss Lab, UW\Skyline-daily.appref-ms" "--in=LorenzoQC.sky,--import=QCReplicate.RAW,--report=Lorenzo SRM QC,--reportfile=QCData.csv,--save"
TODO: Still need to add a full spec of all possible parameters to this issue.
The blog post also describes how to implement automatic updates from code to avoid having the command-line version ever check for updates. This is obviously desirable, and might also allow us to improve the automatic updates to check for updates after start-up, but then offer to restart if updates are required, instead of waiting until the next user initiated restart.